Where is the Tomboy panel applet?
Solution 1:
I'm making the assumption you are running the Unity Interface - if you are using the classic Gnome interface then the following doesnt apply to you.
In Unity, all the previous Gnome Panel applets will not work - except if they were Application Indicators. Unity doesnt allow you to "right click" and add to Panel anymore.
If you start Tom-Boy from the Dash (click the top left 'circle of friends' icon and search from Tom) you should hopefully see the new Tom-Boy Application Indicator displayed in the top-left of the screen.
Add Tom-Boy to the "Startup Applications" so that the Application Indicator is started when you next login.
Solution 2:
Just running Tomboy should load it in the indicator area (it's not an old applet so it doesn't show up in that right click menu anymore):
Solution 3:
Tomboy is not anymore a panel applet (you won't find it in "Add to Panel"), but it will provide an applet in the Indicator area once launched (ALT+F2 "tomboy").
So, if you need the new tomboy applet to be loaded automatically in the Indicator area, you'll need to go to "System/Preferences/Startup Applications" and then "Add", Name: "Tomboy", Command: "tomboy".
This applies to Gnome Desktop AND Unity.
This full solution was already provided in previous answer, but was spread into several answer and comments.